Taylor, you are 100% on the right track. All the answers exist in your question.

#1. These are "redirect notices", not errors. More like warnings.
#2. As long as they are canonicalized correctly, which you said "do I need to do anything if both those pages are canonical to the parent product".

There's absolutely nothing you need to do. You are good. It's always good and important to verify these technical SEO issues. I hope this helps.

I worked on a B2B with a similar problem sometime back. The business decided to implement a Request for Quote system. And there was no impact on the rankings.

I am presuming all those domains are linking to each other, correct ?

Are they regular or nofollow links ? It boils down how much authority you have on your main domain as well as the other domains. If I were you, I will keep the main e-commerce website on one server and everything else including niche blogs etc on a different server. It's not just SEO, but also security issues.

Essentially, to answer your question, it may not be hurting you to have the niche blogs, a forum with user generated content, the articles site and the corporate site on the same IP/server, but it would help you a lot more if they were on a different server, possibly different Class C IPs. So, you will gain from these links being on a different server. Keep in mind, these links are important for you and its good to increase their value by hosting them separately, because these sites are links that your competition can never get linked from. I would also consider doing a nofollow on them, and that's just my thoughts. I prefer lower risk. Again, it depends on what your e-commerce website's link profile is.

I am sure they did, but we were never able to have a read on it because price data was never added to the site. We just started measuring the Call to Action / Conversion as a successful RFQ or a visit to the contact page from these product level pages.

Eric, Have a few questions for you:

1. Do you have executive buy-in to do SEO Work?
2. How much SEO potential is out there for your website to rank?
3. How well does it rank today?
4. How big are your Top 3 competitors? Have they been growing last 1-5 years?

If you can demonstrate the size of the opportunity you have and prove it's achievable with a smaller project, test or experiment, you might have "unlimited resources" ;). Just saying :).

I agree with what you are thinking. The biggest effect would be if you can move them all onto one domain name (sub-folders) and setup 301 redirects. Keep hosting those domains forever since the 301s would stay only as long as you own the domains and continue to host them to serve the 301.

Moving them to sub-domains might be minimal / zero effect. I only see risk in doing that.

Ask yourself: Does it help the users in integrating all the content into one big website ?

Directory links are the "manipulated" links of yesterday. I would strongly suggest to ignore them. Great details Alick300. I would suggest to spend some time reading Moz's Link Building and SEO Guides i.e. http://moz.com/beginners-guide-to-link-building

It's very easy to get in trouble with the wrong links.

I agree with Ian 100%. It does not make sense (Even though that pingback link is nofollowed). Does it help your user ? Would it be useful to have that link available to them ?  Think about the user experience and in most cases, we get the correct answer, which is almost certain to be white hat way of handling the situation :).

Great answer Ian.